Mobile DNA elements are major components of mammalian genomes, accounting for about half of their genetic material. Insertion and rearrangements of mobile elements poses a serious threat to genome stability, and indeed they have been tied to over a hundred human diseases. In recent years there has been a growing appreciation of the long-term influence of mobile elements in shaping genomes and fostering the emergence of biological novelty. But we still have an incomplete and biased picture of the biology and impact of mobile elements in mammals. This is because most of the research has focused on retrotransposons, a prominent class of elements in human and mouse. In this renewal we will pursue our study of another widespread class of elements, the DNA transposons, which remains understudied in mammals. DNA transposons account for 3% of the human genome and at least 12% of the bat genome. They are distinguished from retrotransposons by many facets of their biology and evolutionary dynamics. For instance, we found that some DNA transposons were introduced in diverse mammals by means of horizontal transfer, the passage of genetic material between non-mating species. Thanks to recent technological advances in DNA sequencing and bioinformatics, we are now well positioned to study the incidence and consequences of DNA transposon invasions at a genome-wide scale. In the first aim we will employ a combination of computational and experimental approaches to obtain a quantitative assessment of the frequency and breadth of horizontal transposon transfers in vertebrates. Horizontal transfer of mobile elements is a crucial mechanism for bacterial evolution. Our studies should clarify its evolutionary significance in vertebrates. In th second and third aims we capitalize on the discovery of recent and massive DNA transposon invasions in bats to examine, for the first time in any organism, the contribution of DNA transposons to genomic structural variation (Aim 2) and transcriptome evolution (Aim 3). The development of bats as a mammalian system to study DNA transposons and genome evolution is innovative and it will contribute to a growing body of genomic resources for these emerging models in biomedical research. PUBLIC HEALTH RELEVANCE: In mammalian genomes, including our own, DNA transposons occupy more space than protein-coding sequences. Yet we know surprisingly little about the biology and significance of this class of mobile genetic elements. Here we take advantage of recent breakthroughs in DNA sequencing and bioinformatics to study when and how DNA transposons manage to cross species boundaries via horizontal transfer and how their invasions impact the structure and expression of the mammalian genome.